-You made a great point about bringing Anakin in as a pilot hired to fly Qui Gonn, etc. to Coruscant. I would've liked that more. I preferred an older Anakin in TPM anyway. Though I probably would've switched Tatoonine for Corellia instead. In part because I would've liked to have seen more Star Wars worlds. And I would've switched Alderaan for Naboo. It would've been nice to see more of that world. It perhaps could've added more resonance to Episode IV and been some dreadful foreshadowing of what was to come.

-I don't quite agree with you about Palpatine not wanting the treaty signed. You make some good points though about how it might not have made sense for him to want the treaty to be signed. However if Padme had folded and signed it, I still think he could've engineered a no confidence vote in Valorum using the chancellor's inability to prevent the Trade Federation from forcing Naboo to sign the treaty.

-I too didn't think it made much sense for Dooku to be trying to kill Padme, since she was a strong opponent of the Military Creation Act. What would've made more sense there is for Padme to support the Act. If there had been a Republic military it is doubtful that the Federation would've been able to blockade her planet, so it made no sense for her to be against the act. I think Lucas didn't think that would jibe with her idealism. However I think it would've been great to see Padme unknowingly more complicit in the rise of the Empire too.

-I also thought it would've been sweet if the seeds of the Rebellion were actually the defeated Separatists.

-I also would've not made Dooku a Sith Lord. He was a good Sith Lord. But I liked the idea he floated in AOTC when he was trying to deceive Obi Wan. I think it would've been better if Dooku was actually rebelling against the Republic in a misguided attempt to save it. He would perhaps be a dupe of Palpatine still but for more noble reasons. Or maybe he would just be that one man who could really see what was going on but ultimately powerless to prevent it. And his turning away from the Republic might be better foreshadowing for Anakin's fall.